Control: tags -1 help
On Tue, Jan 14, 2020 at 09:48:10PM +0100, Paul Gevers wrote:
> Did not find CMake 'cmake'
> Found CMake: NO
> Run-time dependency pbbam found: NO
>
> meson.build:54:0: ERROR: Could not generate cargs for pbbam:
> Package pbcopper was not found in the pkg-config search path.
> Perhaps you should add the directory containing `pbcopper.pc'
> to the PKG_CONFIG_PATH environment variable
> Package 'pbcopper', required by 'pbbam', not found
I've fixed this specific issue (and others) in Git[1] but I'm running
into trouble I have no idea to fix.
...
[22/25] c++ -o toAfg 'toAfg@exe/utils_ToAfg.cpp.o' -I/usr/include/pbseq
-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial
-Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wdate-time -
D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=.
-fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1
-std=c++14 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl. a -pthread
-lblasr /usr/lib/x86_64-linux-gnu/libz.so -lpbdata -lpbihdf -lblasr -lpbdata
-lpbihdf -Wl,--end-group '-Wl,-rpath,$ORIGIN/'
-Wl,-rpath-link,/build/blasr-5.3.3+dfsg/build/
FAILED: toAfg
c++ -o toAfg 'toAfg@exe/utils_ToAfg.cpp.o' -I/usr/include/pbseq
-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial
-Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 - g
-O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong
-Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14
-Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a -pthread -lblasr /
usr/lib/x86_64-linux-gnu/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf
-Wl,--end-group '-Wl,-rpath,$ORIGIN/'
-Wl,-rpath-link,/build/blasr-5.3.3+dfsg/build/
/usr/bin/ld: toAfg@exe/utils_ToAfg.cpp.o: undefined reference to symbol
'_ZN6PacBio3BAM9BamRecordD1Ev'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu//libpbbam.so.0.23.0: error adding
symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
In the pbuilder chroot I tried to simplify the linker call and
reduced it to
root@sputnik:/build/blasr-5.3.3+dfsg/build# c++ -o toAfg
'toAfg@exe/utils_ToAfg.cpp.o' -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu
-L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-DHAVE_HDF5_1_10_1 -std=c++14 -lhdf5_cpp -lhdf5 ./libblasr_impl.a -pthread -lz
-lpbdata -lpbihdf -lpbihdf -lblasr
/usr/bin/ld: toAfg@exe/utils_ToAfg.cpp.o: undefined reference to symbol
'_ZN6PacBio3BAM9BamRecordD1Ev'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libpbbam.so.0.23.0: error adding
symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
I've checked that the symbol which is not found exists in the linked
libraries:
root@sputnik:/build/blasr-5.3.3+dfsg/build# grep _ZN6PacBio3BAM9BamRecordD1Ev
/usr/lib/x86_64-linux-gnu/*libpb*
Binary file /usr/lib/x86_64-linux-gnu/libpbbam.so matches
Binary file /usr/lib/x86_64-linux-gnu/libpbbam.so.0.23.0 matches
Binary file /usr/lib/x86_64-linux-gnu/libpbbam.so.1.0.6 matches
Binary file /usr/lib/x86_64-linux-gnu/libpbdata.a matches
Binary file /usr/lib/x86_64-linux-gnu/libpbdata.so matches
I wonder whether the issue might be connected to the fact that there is
only a shared lib but no libpbbam.a (the build system of libpbbam-dev
would need to be tweaked - but I'd assume a shared lib should be
sufficient for linking, right?)
Any hint to fix the build would be welcome.
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/blasr
--
http://fam-tille.de
